4UV4

Crystal structure of anti-FPR Fpro0165 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Affinity Maturation of a Novel Antagonistic Human Monoclonal Antibody with a Long Vh Cdr3 Targeting the Class a Gpcr Formyl-Peptide Receptor 1.

Douthwaite, J.A.Sridharan, S.Huntington, C.Hammersley, J.Marwood, R.Hakulinen, J.K.Ek, M.Sjogren, T.Rider, D.Privezentzev, C.Seaman, J.C.Cariuk, P.Knights, V.Young, J.Wilkinson, T.Sleeman, M.Finch, D.K.Lowe, D.C.Vaughan, T.J.

(2015) MAbs 7: 152

  • DOI: https://doi.org/10.4161/19420862.2014.985158
  • Primary Citation of Related Structures:  
    4UV4

  • PubMed Abstract: 

    Therapeutic monoclonal antibodies targeting G-protein-coupled receptors (GPCRs) are desirable for intervention in a wide range of disease processes. The discovery of such antibodies is challenging due to a lack of stability of many GPCRs as purified proteins. We describe here the generation of Fpro0165, a human anti-formyl peptide receptor 1 (FPR1) antibody generated by variable domain engineering of an antibody derived by immunization of transgenic mice expressing human variable region genes. Antibody isolation and subsequent engineering of affinity, potency and species cross-reactivity using phage display were achieved using FPR1 expressed on HEK cells for immunization and selection, along with calcium release cellular assays for antibody screening. Fpro0165 shows full neutralization of formyl peptide-mediated activation of primary human neutrophils. A crystal structure of the Fpro0165 Fab shows a long, protruding VH CDR3 of 24 amino acids and in silico docking with a homology model of FPR1 suggests that this long VH CDR3 is critical to the predicted binding mode of the antibody. Antibody mutation studies identify the apex of the long VH CDR3 as key to mediating the species cross-reactivity profile of the antibody. This study illustrates an approach for antibody discovery and affinity engineering to typically intractable membrane proteins such as GPCRs.


  • Organizational Affiliation

    a MedImmune Ltd. ; Cambridge , UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FPRO0165 FABA [auth H]243Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FPRO0165 FABB [auth L]219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.35α = 90
b = 128.35β = 90
c = 90.601γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description